Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped20393397.508%
Wrongly Mapped52112.492%
Not Mapped00.0%
Total209144100.0%
Read Failure Statistics
Not mapped00.0%
Missing in mapper output00.0%
Mapped to wrong chromosome32381.548%
Mapped to wrong position19730.943%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment8
Secondary Alignments0
F-Measure0.987400
Precision0.975100
Recall1.000000
Timing
Raw Mapping Time458.040s
Effective Mapping Time453.428s
Effective Init Time4.612s
Effective Time MeasureCPU
Mapping Time (Wall)185.863s
Mapping Time (CPU)458.040s
Mapping Time (CPU User)443.028s
Mapping Time (CPU System)15.012s
Init Time (Wall)4.682s
Init Time (CPU)4.612s
Init Time (CPU User)0.088s
Init Time (CPU System)4.524s
Additional Information
Mapper Memory Usage5617 MB
Total Test Runtime (Wall)229.913s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366548000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.663 sec; CPU: 4.604 sec
systime4.492
time4.6925470829
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366548000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq
[main] Real time: 4.654 sec; CPU: 4.604 sec
systime4.524
time4.68239402771
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq -t 4 > out_bwasw.sam
memory5617604000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 209144 sequences/pairs (31371600 bp) ...
[bsw2_stat] infer the insert size distribution from 23313 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (227, 249, 272)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 362)
[bsw2_stat] mean and std.dev: (249.01, 33.05)
[bsw2_stat] low and high boundaries for proper pairs: (150, 407)
[bsw2_pair] #fixed=5433, #rescued=5, #moved=12
[bsw2_stat] infer the insert size distribution from 23357 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (227, 249, 271)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 359)
[bsw2_stat] mean and std.dev: (249.06, 32.98)
[bsw2_stat] low and high boundaries for proper pairs: (150, 403)
[bsw2_pair] #fixed=5558, #rescued=3, #moved=8
[bsw2_stat] infer the insert size distribution from 23272 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (227, 249, 272)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 362)
[bsw2_stat] mean and std.dev: (249.13, 32.89)
[bsw2_stat] low and high boundaries for proper pairs: (150, 407)
[bsw2_pair] #fixed=5593, #rescued=9, #moved=12
[bsw2_stat] infer the insert size distribution from 23316 high-quality pairs.
[bsw2_stat] (25, 50, 75) percentile: (227, 249, 272)
[bsw2_stat] low and high boundaries for computing mean and std.dev: (150, 362)
[bsw2_stat] mean and std.dev: (249.18, 32.98)
[bsw2_stat] low and high boundaries for proper pairs: (150, 407)
[bsw2_pair] #fixed=5508, #rescued=4, #moved=11
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads1.fastq reads2.fastq
[main] Real time: 185.814 sec; CPU: 458.032 sec
systime15.012
time185.862941027
usrtime443.028
working_directory/project/teaser/genometeaser/tests_generated/9981dd417977dbaa7d58a80ddba44b12